Section is trying to stop a terrorist group from engaging in suicide bombings, and Nikita is assigned to recieve information from an agent known as Formits, who, unbeknownest to Nikita, is in fact a serial killer.

Nikita continues on the mission she was sent on in, "Man in the Middle," which is to marry Helmut Volker, a man with several ties to Red Cell, but she finds out that she is not the only one with secrets, her new husband has a big secret of his own.

Another incursion takes place in Section One, this time in the form of a virus that is making Section One's members sick, one by one. Taking matters into his own hands, George orders in his own Bio Team to treat Section's members. Operations suspects George has an ulterior motive. Sure enough, when Section's people, starting with Walter, followed by Nikita, go in for their ""examination"" with George's Bio Team, they come out vegetables. It seems George's team is mind wiping (downloading the contents of the brains) the Section's members. This process causes them to relive their lives, before leaving them vegetables. Can Michael and Birkoff stop George's team before everyone in Section One gets their brain sucked?

Michael escapes Red Cell and is assigned to meet Nikita and kill her, however she doesn't show up and an Alpha Team is assigned to track her down. Michael leads the team with Kate Quinn. Before the mission, Michael discovers Quinn is Nikita and that he could leave Section. The Alpha Team is wiped out and Michael escapes with Nikita.

Nikita finds clues about why she was recruited into Section. Is it possible her father was an operative, codenamed Flavius, and that she has a sibling with the initial "M" who is somewhere in the covert world she lives in? Quinn redesigns Birkoff's Artificial Intelligence program to build a holographic replica of Madeline, complete with Madeline's memories and psychological profile. Although Operations is greatly pleased to have Madeline at his side once more, it soon becomes clear that despite it's complex programming, it is just not capable of being Madeline because it doesn't have her instincts.